Fixed some type errors

src/hyperion/snapshot_plan.py

@@ -1,6 +1,6 @@
 import bluesky.plan_stubs as bps
 import bluesky.preprocessors as bpp
-from bluesky import RunEngine
+from bluesky.run_engine import RunEngine
 from dodal.devices.aperture import Aperture
 from dodal.devices.backlight import Backlight
 from dodal.devices.oav.oav_detector import OAV

tests/system_tests/experiment_plans/test_plan_system.py

@@ -1,6 +1,6 @@
 import bluesky.preprocessors as bpp
 import pytest
-from bluesky import RunEngine
+from bluesky.run_engine import RunEngine
 from dodal.beamlines import i03
 from dodal.devices.s4_slit_gaps import S4SlitGaps
 from dodal.devices.undulator import Undulator

tests/unit_tests/device_setup_plans/test_setup_oav.py

@@ -26,8 +26,8 @@ def oav() -> OAV:
     oav = i03.oav(fake_with_ophyd_sim=True)
     oav.parameters = OAVConfigParams(ZOOM_LEVELS_XML, DISPLAY_CONFIGURATION)
 
-    oav.proc.port_name.sim_put("proc")
-    oav.cam.port_name.sim_put("CAM")
+    oav.proc.port_name.sim_put("proc")  # type: ignore
+    oav.cam.port_name.sim_put("CAM")  # type: ignore
 
     oav.zoom_controller.zrst.set("1.0x")
     oav.zoom_controller.onst.set("2.0x")
@@ -51,7 +51,7 @@ def fake_smargon() -> Smargon:
     smargon.omega.user_setpoint._use_limits = False
 
     def mock_set(motor, val):
-        motor.user_readback.sim_put(val)
+        motor.user_readback.sim_put(val)  # type: ignore
         return Status(done=True, success=True)
 
     def patch_motor(motor):
@@ -115,7 +115,7 @@ def test_values_for_move_so_that_beam_is_at_pixel(
     oav.parameters.beam_centre_i = beam_centre[0]
     oav.parameters.beam_centre_j = beam_centre[1]
 
-    smargon.omega.user_readback.sim_put(angle)
+    smargon.omega.user_readback.sim_put(angle)  # type: ignore
 
     RE = RunEngine(call_returns_result=True)
     pos = RE(

tests/unit_tests/device_setup_plans/test_topup_plan.py

@@ -4,7 +4,7 @@
 import pytest
 from bluesky.run_engine import RunEngine
 from dodal.beamlines import i03
-from dodal.devices.synchrotron import SynchrotronMode
+from dodal.devices.synchrotron import Synchrotron, SynchrotronMode
 
 from hyperion.device_setup_plans.check_topup import (
     check_topup_and_wait_if_necessary,
@@ -13,16 +13,18 @@
 
 
 @pytest.fixture
-def synchrotron():
+def synchrotron() -> Synchrotron:
     return i03.synchrotron(fake_with_ophyd_sim=True)
 
 
 @patch("hyperion.device_setup_plans.check_topup.wait_for_topup_complete")
 @patch("hyperion.device_setup_plans.check_topup.bps.sleep")
-def test_when_topup_before_end_of_collection_wait(fake_sleep, fake_wait, synchrotron):
-    synchrotron.machine_status.synchrotron_mode.sim_put(SynchrotronMode.USER.value)
-    synchrotron.top_up.start_countdown.sim_put(20.0)
-    synchrotron.top_up.end_countdown.sim_put(60.0)
+def test_when_topup_before_end_of_collection_wait(
+    fake_sleep, fake_wait, synchrotron: Synchrotron
+):
+    synchrotron.machine_status.synchrotron_mode.sim_put(SynchrotronMode.USER.value)  # type: ignore
+    synchrotron.top_up.start_countdown.sim_put(20.0)  # type: ignore
+    synchrotron.top_up.end_countdown.sim_put(60.0)  # type: ignore
 
     RE = RunEngine()
     RE(
@@ -58,8 +60,8 @@ def fake_generator(value):
 
 @patch("hyperion.device_setup_plans.check_topup.bps.sleep")
 @patch("hyperion.device_setup_plans.check_topup.bps.null")
-def test_no_waiting_if_decay_mode(fake_null, fake_sleep, synchrotron):
-    synchrotron.top_up.start_countdown.sim_put(-1)
+def test_no_waiting_if_decay_mode(fake_null, fake_sleep, synchrotron: Synchrotron):
+    synchrotron.top_up.start_countdown.sim_put(-1)  # type: ignore
 
     RE = RunEngine()
     RE(
@@ -74,9 +76,11 @@ def test_no_waiting_if_decay_mode(fake_null, fake_sleep, synchrotron):
 
 
 @patch("hyperion.device_setup_plans.check_topup.bps.null")
-def test_no_waiting_when_mode_does_not_allow_gating(fake_null, synchrotron):
-    synchrotron.top_up.start_countdown.sim_put(1.0)
-    synchrotron.machine_status.synchrotron_mode.sim_put(SynchrotronMode.SHUTDOWN.value)
+def test_no_waiting_when_mode_does_not_allow_gating(
+    fake_null, synchrotron: Synchrotron
+):
+    synchrotron.top_up.start_countdown.sim_put(1.0)  # type: ignore
+    synchrotron.machine_status.synchrotron_mode.sim_put(SynchrotronMode.SHUTDOWN.value)  # type: ignore
 
     RE = RunEngine()
     RE(

tests/unit_tests/device_setup_plans/test_utils.py

@@ -1,7 +1,6 @@
 from unittest.mock import MagicMock
 
 import pytest
-from bluesky import RunEngine
 from bluesky import plan_stubs as bps
 from bluesky.run_engine import RunEngine
 from dodal.beamlines import i03

tests/unit_tests/device_setup_plans/test_xbpm_feedback.py

@@ -20,7 +20,7 @@ def fake_devices():
     attenuator: Attenuator = make_fake_device(Attenuator)(name="atten")
 
     def fake_attenuator_set(val):
-        attenuator.actual_transmission.sim_put(val)
+        attenuator.actual_transmission.sim_put(val)  # type: ignore
         return Status(done=True, success=True)
 
     attenuator.set = MagicMock(side_effect=fake_attenuator_set)
@@ -43,7 +43,7 @@ def my_collection_plan():
         assert xbpm_feedback.pause_feedback.get() == xbpm_feedback.PAUSE
         yield from bps.null()
 
-    xbpm_feedback.pos_stable.sim_put(1)
+    xbpm_feedback.pos_stable.sim_put(1)  # type: ignore
 
     RE = RunEngine()
     RE(my_collection_plan())
@@ -85,7 +85,7 @@ def test_given_xpbm_checks_pass_and_plan_fails_when_plan_run_with_decorator_then
     xbpm_feedback: XBPMFeedback = fake_devices[0]
     attenuator: Attenuator = fake_devices[1]
 
-    xbpm_feedback.pos_stable.sim_put(1)
+    xbpm_feedback.pos_stable.sim_put(1)  # type: ignore
 
     class MyException(Exception):
         pass

tests/unit_tests/experiment_plans/test_grid_detection_plan.py

@@ -39,8 +39,8 @@ def fake_devices(smargon: Smargon, backlight: Backlight, test_config_files):
     oav.mxsc.top.set([0,0,0,0,0,0,0,0,5,5,4,4,3,3,2,2,3,3,4,4])  # noqa: E231
     # fmt: on
 
-    oav.mxsc.pin_tip.tip_x.sim_put(8)
-    oav.mxsc.pin_tip.tip_y.sim_put(5)
+    oav.mxsc.pin_tip.tip_x.sim_put(8)  # type: ignore
+    oav.mxsc.pin_tip.tip_y.sim_put(5)  # type: ignore
 
     oav.parameters = OAVConfigParams(
         test_config_files["zoom_params_file"], test_config_files["display_config"]
@@ -109,8 +109,8 @@ def test_grid_detection_plan_gives_warningerror_if_tip_not_found(
     composite, _ = fake_devices
     oav: OAV = composite.oav
 
-    oav.mxsc.pin_tip.tip_x.sim_put(-1)
-    oav.mxsc.pin_tip.tip_y.sim_put(-1)
+    oav.mxsc.pin_tip.tip_x.sim_put(-1)  # type: ignore
+    oav.mxsc.pin_tip.tip_y.sim_put(-1)  # type: ignore
     oav.mxsc.pin_tip.validity_timeout.put(0.01)
     params = OAVParameters("loopCentring", test_config_files["oav_config_json"])
 

tests/unit_tests/experiment_plans/test_optimise_attenuation_plan.py

@@ -80,7 +80,7 @@ def test_total_counts_calc_new_transmission_raises_warning_on_high_transmission(
     composite: OptimizeAttenuationComposite = fake_create_devices()
     composite.sample_shutter.set = MagicMock(return_value=get_good_status())
     composite.xspress3mini.do_arm.set = MagicMock(return_value=get_good_status())
-    composite.xspress3mini.dt_corrected_latest_mca.sim_put([1, 1, 1, 1, 1, 1])
+    composite.xspress3mini.dt_corrected_latest_mca.sim_put([1, 1, 1, 1, 1, 1])  # type: ignore
     RE(
         total_counts_optimisation(
             composite,
@@ -125,8 +125,8 @@ def test_deadtime_optimisation_calculates_deadtime_correctly(
 ):
     composite: OptimizeAttenuationComposite = fake_create_devices()
 
-    composite.xspress3mini.channel_1.total_time.sim_put(100)
-    composite.xspress3mini.channel_1.reset_ticks.sim_put(101)
+    composite.xspress3mini.channel_1.total_time.sim_put(100)  # type: ignore
+    composite.xspress3mini.channel_1.reset_ticks.sim_put(101)  # type: ignore
     is_deadtime_optimised.return_value = True
 
     with patch(
@@ -207,14 +207,14 @@ def test_total_count_exception_raised_after_max_cycles_reached(RE: RunEngine):
     composite.sample_shutter.set = MagicMock(return_value=get_good_status())
     optimise_attenuation_plan.is_counts_within_target = MagicMock(return_value=False)
     composite.xspress3mini.arm = MagicMock(return_value=get_good_status())
-    composite.xspress3mini.dt_corrected_latest_mca.sim_put([1, 1, 1, 1, 1, 1])
+    composite.xspress3mini.dt_corrected_latest_mca.sim_put([1, 1, 1, 1, 1, 1])  # type: ignore
     with pytest.raises(AttenuationOptimisationFailedException):
         RE(total_counts_optimisation(composite, 1, 0, 10, 0, 5, 2, 1, 0, 0))
 
 
 def test_arm_devices_runs_correct_functions(RE: RunEngine):
     composite: OptimizeAttenuationComposite = fake_create_devices()
-    composite.xspress3mini.detector_state.sim_put("Acquire")
+    composite.xspress3mini.detector_state.sim_put("Acquire")  # type: ignore
     composite.xspress3mini.arm = MagicMock(return_value=get_good_status())
     RE(arm_devices(composite.xspress3mini))
     composite.xspress3mini.arm.assert_called_once()
@@ -248,7 +248,7 @@ def test_total_count_calc_new_transmission_raises_error_on_low_ransmission(
     RE: RunEngine,
 ):
     composite: OptimizeAttenuationComposite = fake_create_devices()
-    composite.xspress3mini.dt_corrected_latest_mca.sim_put([1, 1, 1, 1, 1, 1])
+    composite.xspress3mini.dt_corrected_latest_mca.sim_put([1, 1, 1, 1, 1, 1])  # type: ignore
     composite.sample_shutter.set = MagicMock(return_value=get_good_status())
     composite.xspress3mini.do_arm.set = MagicMock(return_value=get_good_status())
     with pytest.raises(AttenuationOptimisationFailedException):
@@ -276,7 +276,7 @@ def test_total_counts_gets_within_target(mock_arm_devices, RE: RunEngine):
     def update_data(_):
         nonlocal iteration
         iteration += 1
-        composite.xspress3mini.dt_corrected_latest_mca.sim_put(
+        composite.xspress3mini.dt_corrected_latest_mca.sim_put(  # type: ignore
             ([50, 50, 50, 50, 50]) * iteration
         )
         return get_good_status()

tests/unit_tests/experiment_plans/test_pin_tip_centring.py

@@ -25,9 +25,9 @@ def get_fake_pin_values_generator(x, y):
 def test_given_the_pin_tip_is_already_in_view_when_get_tip_into_view_then_tip_returned_and_smargon_not_moved(
     smargon: Smargon, oav: OAV, RE: RunEngine
 ):
-    smargon.x.user_readback.sim_put(0)
-    oav.mxsc.pin_tip.tip_x.sim_put(100)
-    oav.mxsc.pin_tip.tip_y.sim_put(200)
+    smargon.x.user_readback.sim_put(0)  # type: ignore
+    oav.mxsc.pin_tip.tip_x.sim_put(100)  # type: ignore
+    oav.mxsc.pin_tip.tip_y.sim_put(200)  # type: ignore
 
     oav.mxsc.pin_tip.trigger = MagicMock(side_effect=oav.mxsc.pin_tip.trigger)
 
@@ -44,14 +44,14 @@ def test_given_no_tip_found_but_will_be_found_when_get_tip_into_view_then_smargo
     RE: RunEngine,
 ):
     oav.mxsc.pin_tip.settle_time_s.put(0.01)
-    smargon.x.user_setpoint.sim_set_limits([-2, 2])
+    smargon.x.user_setpoint.sim_set_limits([-2, 2])  # type: ignore
     oav.mxsc.pin_tip.triggered_tip.put(oav.mxsc.pin_tip.INVALID_POSITION)
     oav.mxsc.pin_tip.validity_timeout.put(0.015)
-    smargon.x.user_readback.sim_put(0)
+    smargon.x.user_readback.sim_put(0)  # type: ignore
 
     def set_pin_tip_when_x_moved(*args, **kwargs):
-        oav.mxsc.pin_tip.tip_x.sim_put(100)
-        oav.mxsc.pin_tip.tip_y.sim_put(200)
+        oav.mxsc.pin_tip.tip_x.sim_put(100)  # type: ignore
+        oav.mxsc.pin_tip.tip_y.sim_put(200)  # type: ignore
 
     smargon.x.subscribe(set_pin_tip_when_x_moved, run=False)
 
@@ -65,16 +65,16 @@ def test_given_tip_at_zero_but_will_be_found_when_get_tip_into_view_then_smargon
     smargon: Smargon, oav: OAV, RE: RunEngine
 ):
     oav.mxsc.pin_tip.settle_time_s.put(0.01)
-    smargon.x.user_setpoint.sim_set_limits([-2, 2])
-    oav.mxsc.pin_tip.tip_x.sim_put(0)
-    oav.mxsc.pin_tip.tip_y.sim_put(100)
+    smargon.x.user_setpoint.sim_set_limits([-2, 2])  # type: ignore
+    oav.mxsc.pin_tip.tip_x.sim_put(0)  # type: ignore
+    oav.mxsc.pin_tip.tip_y.sim_put(100)  # type: ignore
     oav.mxsc.pin_tip.validity_timeout.put(0.15)
 
-    smargon.x.user_readback.sim_put(0)
+    smargon.x.user_readback.sim_put(0)  # type: ignore
 
     def set_pin_tip_when_x_moved(*args, **kwargs):
-        oav.mxsc.pin_tip.tip_y.sim_put(200)
-        oav.mxsc.pin_tip.tip_x.sim_put(100)
+        oav.mxsc.pin_tip.tip_y.sim_put(200)  # type: ignore
+        oav.mxsc.pin_tip.tip_x.sim_put(100)  # type: ignore
 
     smargon.x.subscribe(set_pin_tip_when_x_moved, run=False)
 
@@ -93,9 +93,9 @@ def test_pin_tip_starting_near_negative_edge_doesnt_exceed_limit(
         get_fake_pin_values_generator(0, 100),
     ]
 
-    smargon.x.user_setpoint.sim_set_limits([-2, 2])
-    smargon.x.user_setpoint.sim_put(-1.8)
-    smargon.x.user_readback.sim_put(-1.8)
+    smargon.x.user_setpoint.sim_set_limits([-2, 2])  # type: ignore
+    smargon.x.user_setpoint.sim_put(-1.8)  # type: ignore
+    smargon.x.user_readback.sim_put(-1.8)  # type: ignore
 
     with pytest.raises(WarningException):
         RE(move_pin_into_view(oav, smargon, max_steps=1))
@@ -114,9 +114,9 @@ def test_pin_tip_starting_near_positive_edge_doesnt_exceed_limit(
         get_fake_pin_values_generator(-1, -1),
         get_fake_pin_values_generator(-1, -1),
     ]
-    smargon.x.user_setpoint.sim_set_limits([-2, 2])
-    smargon.x.user_setpoint.sim_put(1.8)
-    smargon.x.user_readback.sim_put(1.8)
+    smargon.x.user_setpoint.sim_set_limits([-2, 2])  # type: ignore
+    smargon.x.user_setpoint.sim_put(1.8)  # type: ignore
+    smargon.x.user_readback.sim_put(1.8)  # type: ignore
 
     with pytest.raises(WarningException):
         RE(move_pin_into_view(oav, smargon, max_steps=1))
@@ -127,11 +127,11 @@ def test_pin_tip_starting_near_positive_edge_doesnt_exceed_limit(
 def test_given_no_tip_found_ever_when_get_tip_into_view_then_smargon_moved_positive_and_exception_thrown(
     smargon: Smargon, oav: OAV, RE: RunEngine
 ):
-    smargon.x.user_setpoint.sim_set_limits([-2, 2])
+    smargon.x.user_setpoint.sim_set_limits([-2, 2])  # type: ignore
     oav.mxsc.pin_tip.triggered_tip.put(oav.mxsc.pin_tip.INVALID_POSITION)
     oav.mxsc.pin_tip.validity_timeout.put(0.01)
 
-    smargon.x.user_readback.sim_put(0)
+    smargon.x.user_readback.sim_put(0)  # type: ignore
 
     with pytest.raises(WarningException):
         RE(move_pin_into_view(oav, smargon))
@@ -142,7 +142,7 @@ def test_given_no_tip_found_ever_when_get_tip_into_view_then_smargon_moved_posit
 def test_given_moving_out_of_range_when_move_with_warn_called_then_warning_exception(
     RE: RunEngine, smargon: Smargon
 ):
-    smargon.x.high_limit_travel.sim_put(10)
+    smargon.x.high_limit_travel.sim_put(10)  # type: ignore
 
     with pytest.raises(WarningException):
         RE(move_smargon_warn_on_out_of_range(smargon, (100, 0, 0)))
@@ -183,7 +183,7 @@ def test_when_pin_tip_centre_plan_called_then_expected_plans_called(
     test_config_files,
     RE,
 ):
-    smargon.omega.user_readback.sim_put(0)
+    smargon.omega.user_readback.sim_put(0)  # type: ignore
     mock_oav = MagicMock(spec=OAV)
     mock_oav.parameters = OAVConfigParams(
         test_config_files["zoom_params_file"], test_config_files["display_config"]

tests/unit_tests/experiment_plans/test_rotation_scan_plan.py

@@ -507,7 +507,7 @@ def test_acceleration_offset_calculated_correctly(
     undulator: Undulator,
     flux: Flux,
 ):
-    smargon.omega.acceleration.sim_put(0.2)
+    smargon.omega.acceleration.sim_put(0.2)  # type: ignore
     setup_and_run_rotation_plan_for_tests(
         RE,
         test_rotation_params,

tests/unit_tests/external_interaction/callbacks/test_rotation_callbacks.py

@@ -135,7 +135,7 @@ def test_nexus_handler_gets_documents_in_mock_plan(
 )
 def test_nexus_handler_only_writes_once(
     ispyb,
-    nexus_writer,
+    nexus_writer: MagicMock,
     RE: RunEngine,
     params: RotationInternalParameters,
     test_start_doc,
@@ -197,7 +197,7 @@ def test_nexus_handler_triggers_write_file_when_told(
 )
 def test_zocalo_start_and_end_triggered_once(
     ispyb,
-    zocalo,
+    zocalo: MagicMock,
     RE: RunEngine,
     params: RotationInternalParameters,
 ):